Director-General of NBC, Modibbo Kawu, announced the shutdown on Thursday evening.
He said the action was taken for failure of the TV and radio stations to abide by the broadcasting code.
Daar Communications Founder, Raymond Dokpesi, had earlier accused the Presidency of intimidating his media group.
He made the allegation while speaking at a press conference in the company's corporate headquarters in Abuja on Thursday.
"I have it on strict authority and very assured information that the highest echelon of the government, the Presidency, queried and challenged the NBC that they were not doing their jobs: 'How on earth could they be hearing and seeing on AIT what they termed hate speech?
"Any criticism of this government is hate speech. The NBC is acting under the authority of the President and Commander-in-Chief. The licensing fees in Nigeria is one of the highest in the world. There is no country in the world where you have this type of exploitative fees. I have appealed for a reduction because the payments cannot be sustained by private broadcasters in Nigeria."